I recently read an interesting article over on NPR's site, called Why We Need A Science Capable Of Explaining Itself. It was an interesting read in which the author, Marcelo Gleiser, makes the assertion that big science (cosmology) and religion can exist side-by-side as long as science admits that it can't explain everything. However, I would argue that the author makes the mistake of confusing the tool with the product. He argues a few points successfully.
First, that as humans we are integral parts of the Universe we are trying to explain. The argument is that we can't get enough outside ourselves and the Universe we inhabit to make meaningful judgements. In other words: To a worm, everything looks like dirt. I've often thought that our physics is like living in a closet guessing at what the rest of the house may look like.
The second is that our tool for measurement, science, is inherently a part of us as integral components of the universe we inhabit. It's like using a yardstick to measure the length of another yardstick. I think he misses the point a bit here because what science uncovers is internal consistencies - starting with F = MA leading up to E = MC2 and through Quantum Mechanics. Another way of looking at this is that we are merely holding the Universe accountable for being consistent so that we can make predictions about similar outcomes as they arise from similar antecedents.
The final point he makes is that we postulate that the Universe suddenly erupted from nothing and that we can't explain the antecedent to the Big Bang. If you keep asking "why?" both science and religion end up at the same point. Because we can't step outside our existence enough to be cosmologically empirical and because we are using the Universe to measure the Universe, our measurements become increasingly suspect as we approach the edge cases of the Big Bang, the Big Crunch, and the event horizons of black holes.
Alternative: The Big Flush
In the Beginning, there was Darkness...
The current common wisdom says there was nothing then, in an instant, there was everything. It exploded from some point and in an inflationary instant, irregularities were created that formed the galaxies, then suns, then planets... We look around us and this appears to be true. Stars in all directions seem to be red-shifted, so they must be moving away from us. The analogy is that of a balloon. That we are riding the surface of a cosmic bubble and as it expands, all things are moving away from us. This is consistent with biblical thinking regarding "Let there be light." And holds together under our desire for the Universe to be consistent.
... or maybe, it was just gray.
Another article I read recently discussed a team of scientists in Denmark discussing the possibility that the Universe was already collapsing.
It is equally valid to think that the Universe was derived from everything... That in the beginning, there wasn't darkness but infinite gray. What if at the outset of our Universe, it was completely filled with quantum foam - virtual particles popping in and out of existence more-or-less evenly throughout the Universe? What if the Big Bang wasn't space and time erupting from some central point, but was a rupture in the fabric of space-time? Think of the same balloon, but instead of it inflating almost instantaneously, it was already full and the primary cosmic event was a pin-prick in the surface. Imagine that we are not on the outside of the balloon, but the inside. While the shell of the Universe is collapsing, the air inside is becoming more and more diffuse. To those particles, it would still look like the individual components of the Universe were moving apart, even though the universe as a whole was collapsing.
Even if there were multiple ruptures, the Universe would still behave as if it were expanding because the air inside the balloon would be getting less dense all the time, and the reduction in density would accelerate as the pressure of the balloon pushed in on increasingly less dense air. The problems arise from assuming there is a center to the Universe and that the fundamental event of creation occurred there. We can avoid Cosmological Constant type fudge factors if we remove a central point from the model.
It is possible that all our Universe has ever known is collapse. Maybe, time is an effect of gravity due to the rupturing of our space-time by an adjacent Universe.